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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
469
ChIP-seq
112
total RNA-seq
28
ATAC-seq
6
MeRIP-seq
6
pCHi-C
5
STARR-seq
3
CRISPR genome editing followed by DNA sequencing
3
Hi-C
2
Capture-C
2
DNase-seq
2
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
469
DNA binding
114
Transcription
30
DNA accessibility
3
3D chromatin structure
1
DNA sequencing
Target of assay
360
transcription factor
89
recombinant protein
81
control
64
RNA binding protein
30
chromatin remodeller
28
histone
28
histone modification
15
narrow histone mark
13
broad histone mark
3
nucleotide modification
other context
2
other post-translational modification
Date released
313
November, 2017
96
February, 2021
60
November, 2018
44
August, 2021
30
October, 2019
28
December, 2018
23
January, 2019
21
May, 2021
November, 2019
11
March, 2020
6
February, 2023
6
November, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
565
bam
508
bigWig
425
fastq
390
bed narrowPeak
353
bigBed narrowPeak
118
tsv
58
bed broadPeak
58
bigBed broadPeak
20
tagAlign
3
bed bed3+
3
tar
1
bed bed3
bed bedMethyl
1
bedpe bed3+
1
bigBed bedMethyl
1
hdf5
1
hic
1
txt
1
vcf
Organism
639
Homo sapiens
Biosample type
2707
tissue
1078
primary cell
643
cell line
389
in vitro differentiated cells
10
stem cell
Organ
398
liver
76
pancreas
66
artery
66
blood vessel
66
heart
66
vasculature
63
epithelium
61
blood
61
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
632
AMP
9
T1D
2
community
Genome assembly (visualization)
514
hg19
448
GRCh38
Lab
596
AMP-T2D consortium
34
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
76
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
13
missing controlled_by
Audit category:
26
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
files.file_type!
bed bedMethyl
month_released!
November, 2019
organ_slims!
thymus
target.investigated_as!
other context
BIOSAMPLE
ASSAY
643 results
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ChIP-seq
total RNA-seq
ATAC-seq
MeRIP-seq
pCHi-C
STARR-seq
CRISPR genome editing followed by DNA sequencing
Hi-C
Capture-C
DNase-seq
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
376
14
1
2
2
2
1
EndoC_BH1
2
32
18
6
3
2
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
60
1
Panc1
13
1
1
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